RetrogeneDB ID: retro_chof_1422

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_288656:820..1566(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSCHOG00000006998
• Aliases: None
• Description: cancer susceptibility candidate 4 [Source:HGNC Symbol;Acc:24892]

Sequence

>retro_chof_1422
GTTAAACTACACAGCAACATATTACATCAAATGGCAGACATATGTCATTTAAAGGAGCAACTTGCTGAGCTTTGTCAGGA
GTTTCTTCAACAAGACCAGCTGCACGACAACAAGAAAAATAATACTTAACTCCTGAAGAGGTTAGAATATGAGAGCTTAC
AGTGTGGACAACAGATAAAGGAATTAAGAACACAGCATGAAGCAAATATTAAAAAGTTAGCAGATCAGATTTTGCAGGAA
CAAAAACAAGAGGTGCACAAGGTTCAGTCAAATGATGGCAATGATTTGGGTATAAATGATAATGCAGTACCTAAAAATAT
TCCAAAAGTAGCTGAGAATGCTGCAGATAAGAATGAAGAGCCTTCAAGCCATCATATTCCATGTGGAAAAGAACAAATCA
AATGAGGTGATGATTCAGAGATGTCTGGGATAGAAGAGAATGAACTTGTAAAAGTTGAAGATCTTCCCACTTCTTTAAAG
AAGCCCCCCTTTCAGTTTCTAAACATGAAAGTCATCAAGCAATCTCTCATCTTCGAACTGGAAAAGCTCTCTCCTCAGAT
ATGGCTCCAGGTTCACAAATGAACCACAATCGAAATCCTGGTACTTCAAAACAGATATCATCTAACTCCCTTCAGCGTTT
AATTCCAGGCTCAAACTTGGAAAGTGAACCCAGAGTTCAAACAGATATGCTAAAGCAGGATACCTAGGATACAGTTGGTG
ATTTACATAAATTGAAGCAAAGTAAG

Alignment

ORF - retro_chof_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 82.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKLQNNISYQMADIHHLKEQLAELRQEFLRQEDQLQDYRKNNTYXXXXXXXXXFQCGQQIKELRTQHEEN
          VKL..NI..QMADI.HLKEQLAEL.QEFL.Q.DQL.D..KNNT...........QCGQQIKELRTQHE.N
Retrocopy VKLHSNILHQMADICHLKEQLAELCQEFL-QQDQLHDNKKNNT*LLKRLEYESLQCGQQIKELRTQHEAN

Parental  IKKLADQFVQEQKQEMHKVQSNDDKDLGINDHAVPKNIPKVAENAADKNEEPSSNHILHGKEHIKRGGDA
          IKKLADQ..QEQKQE.HKVQSND..DLGIND.AVPKNIPKVAENAADKNEEPSS.HI..GKE.IK.G.D.
Retrocopy IKKLADQILQEQKQEVHKVQSNDGNDLGINDNAVPKNIPKVAENAADKNEEPSSHHIPCGKEQIK*GDDS

Parental  GMPGIEENDLAKAEDLPTSLKKP-PLSVSKHGSHQAISRLATGQPLSPNMAPDSQMNHNRNPGTSKQISS
          .M.GIEEN.L.K.EDLPTSLKKP.PLSVSKH.SHQAIS.L.TG..LS..MAP.SQMNHNRNPGTSKQISS
Retrocopy EMSGIEENELVKVEDLPTSLKKP<PLSVSKHESHQAISHLRTGKALSSDMAPGSQMNHNRNPGTSKQISS

Parental  NSLQRLIPGPNLESEPRVQTDMLKQDTKDRVGDFHKLKQSR
          NSLQRLIPG.NLESEPRVQTDMLKQDT.D.VGD.HKLKQS.
Retrocopy NSLQRLIPGSNLESEPRVQTDMLKQDT*DTVGDLHKLKQSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1422 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422 , retro_chof_1445, retro_chof_2453, retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852,